Microarrays最新文献_第3页

Living Cell Microarrays: An Overview of Concepts. 活细胞微阵列:概念概述。

Microarrays Pub Date : 2016-05-26 DOI: 10.3390/microarrays5020011

Rebecca Jonczyk, Tracy Kurth, Antonina Lavrentieva, Johanna-Gabriela Walter, Thomas Scheper, Frank Stahl

{"title":"Living Cell Microarrays: An Overview of Concepts.","authors":"Rebecca Jonczyk, Tracy Kurth, Antonina Lavrentieva, Johanna-Gabriela Walter, Thomas Scheper, Frank Stahl","doi":"10.3390/microarrays5020011","DOIUrl":"10.3390/microarrays5020011","url":null,"abstract":"Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34366382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 35

Stromal Activation by Tumor Cells: An in Vitro Study in Breast Cancer. 肿瘤细胞激活基质:乳腺癌的体外研究。

Microarrays Pub Date : 2016-05-18 DOI: 10.3390/microarrays5020010

Giuseppe Merlino, Patrizia Miodini, Biagio Paolini, Maria Luisa Carcangiu, Massimiliano Gennaro, Matteo Dugo, Maria Grazia Daidone, Vera Cappelletti

{"title":"Stromal Activation by Tumor Cells: An in Vitro Study in Breast Cancer.","authors":"Giuseppe Merlino, Patrizia Miodini, Biagio Paolini, Maria Luisa Carcangiu, Massimiliano Gennaro, Matteo Dugo, Maria Grazia Daidone, Vera Cappelletti","doi":"10.3390/microarrays5020010","DOIUrl":"https://doi.org/10.3390/microarrays5020010","url":null,"abstract":"Background: The tumor microenvironment participates in the regulation of tumor progression and influences treatment sensitivity. In breast cancer, it also may play a role in determining the fate of non-invasive lesions such as ductal carcinoma in situ (DCIS), a non-obligate precursor of invasive diseases, which is aggressively treated despite its indolent nature in many patients since no biomarkers are available to predict the progression of DCIS to invasive disease. In vitro models of stromal activation by breast tumor cells might provide clues as to specific stromal genes crucial for the transition from DCIS to invasive disease.Methods: normal human dermal fibroblasts (NHDF) were treated under serum-free conditions with cell culture media conditioned by breast cancer cell lines (SkBr3, MDA-MB-468, T47D) for 72 h and subjected to gene expression profiling with Illumina platform.Results: TGM2, coding for a tissue transglutaminase, was identified as candidate gene for stromal activation. In public transcriptomic datasets of invasive breast tumors TGM2 expression proved to provide prognostic information. Conversely, its role as an early biosensor of tumor invasiveness needs to be further investigated by in situ analyses.Conclusion: Stromal TGM2 might probably be associated with precancerous evolution at earlier stages compared to DCIS.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34421562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Microarray-Based Comparative Genomic and Transcriptome Analysis of Borrelia burgdorferi. 基于微阵列的伯氏疏螺旋体比较基因组和转录组分析。

Microarrays Pub Date : 2016-04-16 DOI: 10.3390/microarrays5020009

Radha Iyer, Ira Schwartz

{"title":"Microarray-Based Comparative Genomic and Transcriptome Analysis of Borrelia burgdorferi.","authors":"Radha Iyer, Ira Schwartz","doi":"10.3390/microarrays5020009","DOIUrl":"https://doi.org/10.3390/microarrays5020009","url":null,"abstract":"Borrelia burgdorferi, the spirochetal agent of Lyme disease, is maintained in nature in a cycle involving a tick vector and a mammalian host. Adaptation to the diverse conditions of temperature, pH, oxygen tension and nutrient availability in these two environments requires the precise orchestration of gene expression. Over 25 microarray analyses relating to B. burgdorferi genomics and transcriptomics have been published. The majority of these studies has explored the global transcriptome under a variety of conditions and has contributed substantially to the current understanding of B. burgdorferi transcriptional regulation. In this review, we present a summary of these studies with particular focus on those that helped define the roles of transcriptional regulators in modulating gene expression in the tick and mammalian milieus. By performing comparative analysis of results derived from the published microarray expression profiling studies, we identified composite gene lists comprising differentially expressed genes in these two environments. Further, we explored the overlap between the regulatory circuits that function during the tick and mammalian phases of the enzootic cycle. Taken together, the data indicate that there is interplay among the distinct signaling pathways that function in feeding ticks and during adaptation to growth in the mammal. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34421561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 23

Time-Resolved Study of Nanoparticle Induced Apoptosis Using Microfabricated Single Cell Arrays. 纳米颗粒诱导细胞凋亡的时间分辨研究。

Microarrays Pub Date : 2016-04-15 DOI: 10.3390/microarrays5020008

Peter J F Röttgermann, Kenneth A Dawson, Joachim O Rädler

{"title":"Time-Resolved Study of Nanoparticle Induced Apoptosis Using Microfabricated Single Cell Arrays.","authors":"Peter J F Röttgermann, Kenneth A Dawson, Joachim O Rädler","doi":"10.3390/microarrays5020008","DOIUrl":"https://doi.org/10.3390/microarrays5020008","url":null,"abstract":"Cell fate decisions like apoptosis are heterogeneously implemented within a cell population and, consequently, the population response is recognized as sum of many individual dynamic events. Here, we report on the use of micro-patterned single-cell arrays for real-time tracking of nanoparticle-induced (NP) cell death in sets of thousands of cells in parallel. Annexin (pSIVA) and propidium iodide (PI), two fluorescent indicators of apoptosis, are simultaneously monitored after exposure to functionalized polystyrene (PS - NH 2) nanobeads as a model system. We find that the distribution of Annexin onset times shifts to later times and broadens as a function of decreasing NP dose. We discuss the mean time-to-death as a function of dose, and show how the EC 50 value depends both on dose and time of measurement. In addition, the correlations between the early and late apoptotic markers indicate a systematic shift from apoptotic towards necrotic cell death during the course of the experiment. Thus, our work demonstrates the potential of array-based single cell cytometry for kinetic analysis of signaling cascades in a high-throughput format. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34421560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

A Double-Hybridization Approach for the Transcription- and Amplification-Free Detection of Specific mRNA on a Microarray. 一种双杂交方法用于基因芯片上特异性mRNA的转录和扩增检测。

Microarrays Pub Date : 2016-02-23 DOI: 10.3390/microarrays5010005

Michaela Haider, Thomas Haselgrübler, Alois Sonnleitner, Fritz Aberger, Jan Hesse

{"title":"A Double-Hybridization Approach for the Transcription- and Amplification-Free Detection of Specific mRNA on a Microarray.","authors":"Michaela Haider, Thomas Haselgrübler, Alois Sonnleitner, Fritz Aberger, Jan Hesse","doi":"10.3390/microarrays5010005","DOIUrl":"https://doi.org/10.3390/microarrays5010005","url":null,"abstract":"A double-hybridization approach was developed for the enzyme-free detection of specific mRNA of a housekeeping gene. Targeted mRNA was immobilized by hybridization to complementary DNA capture probes spotted onto a microarray. A second hybridization step of Cy5-conjugated label DNA to another section of the mRNA enabled specific labeling of the target. Thus, enzymatic artifacts could be avoided by omitting transcription and amplification steps. This manuscript describes the development of capture probe molecules used in the transcription- and amplification-free analysis of RPLP0 mRNA in isolated total RNA. An increase in specific signal was found with increasing length of the target-specific section of capture probes. Unspecific signal comprising spot autofluorescence and unspecific label binding did not correlate with the capture length. An additional spacer between the specific part of the capture probe and the substrate attachment site increased the signal significantly only on a short capture probe of approximately 30 nt length. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5010005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34421559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Glycoarray Technologies: Deciphering Interactions from Proteins to Live Cell Responses. 糖阵列技术:解读从蛋白质到活细胞反应的相互作用。

Microarrays Pub Date : 2016-01-04 DOI: 10.3390/microarrays5010003

Tania M Puvirajesinghe, Jeremy E Turnbull

引用次数: 24

Identification of Critical Region Responsible for Split Hand/Foot Malformation Type 3 (SHFM3) Phenotype through Systematic Review of Literature and Mapping of Breakpoints Using Microarray Data. 通过系统的文献回顾和利用微阵列数据绘制断点，确定掌/足分叉畸形3型(SHFM3)表型的关键区域。

Microarrays Pub Date : 2015-12-24 DOI: 10.3390/microarrays5010002

Catherine F Li, Katie Angione, Jeff M Milunsky

{"title":"Identification of Critical Region Responsible for Split Hand/Foot Malformation Type 3 (SHFM3) Phenotype through Systematic Review of Literature and Mapping of Breakpoints Using Microarray Data.","authors":"Catherine F Li, Katie Angione, Jeff M Milunsky","doi":"10.3390/microarrays5010002","DOIUrl":"https://doi.org/10.3390/microarrays5010002","url":null,"abstract":"Split hand/foot malformation (SHFM) is a limb malformation with underdeveloped or absent central digital rays, clefts of hands and feet, and variable syndactyly of the remaining digits. There are six types of SHFM. Here, we report a boy with SHFM type 3 having normal 4th and 5th digits, absent 2nd and 3rd digits, and a 4th finger flexion deformity, as well as absent 2nd, 3rd and 4th toes bilaterally. His father, two paternal uncles, and two paternal first cousins have similar phenotype. Chromosome analysis showed a normal male karyotype. A 514 kb gain at 10q24.31-q24.32 (chr10:102,962,134-103,476,346, hg19) was identified using 6.0 Single nucleotide polymorphism (SNP) microarray, resulting in the duplication of nine genes, including BTRC and FBXW4. A detailed systematic review of literature and mapping of breakpoints using microarray data from all reported cases in PubMed and DECIPHER were conducted, and exon 1 of BTRC gene was identified as the critical region responsible for the SHFM3 phenotype. The potential mechanism and future studies of this critical region causing the SHFM3 phenotype are discussed. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5010002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34421556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

SNP Array in Hematopoietic Neoplasms: A Review. 造血肿瘤SNP阵列研究进展

Microarrays Pub Date : 2015-12-22 DOI: 10.3390/microarrays5010001

Jinming Song, Haipeng Shao

{"title":"SNP Array in Hematopoietic Neoplasms: A Review.","authors":"Jinming Song, Haipeng Shao","doi":"10.3390/microarrays5010001","DOIUrl":"https://doi.org/10.3390/microarrays5010001","url":null,"abstract":"Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH) studies. Single nucleotide polymorphism (SNP) arrays offer high-resolution identification of copy number variants (CNVs) and acquired copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD) that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5010001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34421557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 16

Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays. 利用基于碳水化合物的微阵列评估细菌相互作用。

Microarrays Pub Date : 2015-12-10 DOI: 10.3390/microarrays4040690

Andrea Flannery, Jared Q Gerlach, Lokesh Joshi, Michelle Kilcoyne

{"title":"Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays.","authors":"Andrea Flannery, Jared Q Gerlach, Lokesh Joshi, Michelle Kilcoyne","doi":"10.3390/microarrays4040690","DOIUrl":"https://doi.org/10.3390/microarrays4040690","url":null,"abstract":"Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i) conventional carbohydrate or glycan microarrays; (ii) whole mucin microarrays; and (iii) microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"4 4","pages":"690-713"},"PeriodicalIF":0.0,"publicationDate":"2015-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays4040690","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34712581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

Mining the Dynamic Genome: A Method for Identifying Multiple Disease Signatures Using Quantitative RNA Expression Analysis of a Single Blood Sample. 挖掘动态基因组:一种利用单个血液样本定量RNA表达分析识别多种疾病特征的方法。

Microarrays Pub Date : 2015-12-10 DOI: 10.3390/microarrays4040671

Samuel Chao, Changming Cheng, Choong-Chin Liew

{"title":"Mining the Dynamic Genome: A Method for Identifying Multiple Disease Signatures Using Quantitative RNA Expression Analysis of a Single Blood Sample.","authors":"Samuel Chao, Changming Cheng, Choong-Chin Liew","doi":"10.3390/microarrays4040671","DOIUrl":"https://doi.org/10.3390/microarrays4040671","url":null,"abstract":"Background: Blood has advantages over tissue samples as a diagnostic tool, and blood mRNA transcriptomics is an exciting research field. To realize the full potential of blood transcriptomic investigations requires improved methods for gene expression measurement and data interpretation able to detect biological signatures within the \"noisy\" variability of whole blood.Methods: We demonstrate collection tube bias compensation during the process of identifying a liver cancer-specific gene signature. The candidate probe set list of liver cancer was filtered, based on previous repeatability performance obtained from technical replicates. We built a prediction model using differential pairs to reduce the impact of confounding factors. We compared prediction performance on an independent test set against prediction on an alternative model derived by Weka. The method was applied to an independent set of 157 blood samples collected in PAXgene tubes.Results: The model discriminated liver cancer equally well in both EDTA and PAXgene collected samples, whereas the Weka-derived model (using default settings) was not able to compensate for collection tube bias. Cross-validation results show our procedure predicted membership of each sample within the disease groups and healthy controls.Conclusion: Our versatile method for blood transcriptomic investigation overcomes several limitations hampering research in blood-based gene tests.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"4 4","pages":"671-89"},"PeriodicalIF":0.0,"publicationDate":"2015-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays4040671","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34712580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7